diff --git a/DEVELOPER_NOTES.md b/DEVELOPER_NOTES.md
index 1c13e5a8b..f183184d3 100644
--- a/DEVELOPER_NOTES.md
+++ b/DEVELOPER_NOTES.md
@@ -232,4 +232,8 @@ e.g. Set overdue status for overdue invoices on auth account 1234.
 `python3 invoke_jobs.py STATEMENTS_DUE OVERDUE 2024-10-15 1234`
 
 Date Override: The date you want to emulate the job is running on.
-Account Id: The auth account id to run the job against.
\ No newline at end of file
+Account Id: The auth account id to run the job against.
+
+
+24. How do I manually apply an eft payment to a specific statement?
+Here: https://drive.google.com/file/d/12WqEis2rQMyKHFNitZRukXWlSLKTa-x1/view?usp=drive_link
\ No newline at end of file
diff --git a/pay-queue/src/pay_queue/services/eft/eft_reconciliation.py b/pay-queue/src/pay_queue/services/eft/eft_reconciliation.py
index 74532644f..eaba12a67 100644
--- a/pay-queue/src/pay_queue/services/eft/eft_reconciliation.py
+++ b/pay-queue/src/pay_queue/services/eft/eft_reconciliation.py
@@ -203,6 +203,11 @@ def _apply_eft_pending_payments(context: EFTReconciliation, shortname_balance):
 
         eft_credit_balance = EFTCreditModel.get_eft_credit_balance(eft_short_name.id)
         shortname_links = EFTShortnamesService.get_shortname_links(eft_short_name.id).get("items", [])
+
+        # Don't apply auto payments for multi link accounts
+        if len(shortname_links) > 1:
+            continue
+
         for shortname_link in shortname_links:
             # We are expecting pending payments to have been cleared since this runs after the
             # eft task job. Something may have gone wrong, we will skip this link.
diff --git a/pay-queue/tests/integration/test_eft_reconciliation.py b/pay-queue/tests/integration/test_eft_reconciliation.py
index 4b6707b17..cd40ae87d 100644
--- a/pay-queue/tests/integration/test_eft_reconciliation.py
+++ b/pay-queue/tests/integration/test_eft_reconciliation.py
@@ -1063,6 +1063,40 @@ def test_apply_pending_payments(session, app, client):
     assert short_name_link.get("amount_owing") == 150.50
 
 
+def test_multi_link_apply_pending_payments(session, app, client):
+    """Test automatic payments do not apply to multi link accounts."""
+    payment_account, eft_short_name, invoice = create_test_data()
+    payment_account_2 = factory_create_eft_account(auth_account_id="2222")
+    EFTShortnameLinksModel(
+        eft_short_name_id=eft_short_name.id,
+        auth_account_id=payment_account_2.auth_account_id,
+        status_code=EFTShortnameStatus.LINKED.value,
+        updated_by="TEST",
+        updated_by_name="TEST",
+        updated_on=datetime.now(),
+    ).save()
+    create_statement_from_invoices(payment_account, [invoice])
+    file_name: str = "test_eft_tdi17.txt"
+    generate_tdi17_file(file_name)
+
+    add_file_event_to_queue_and_process(
+        client,
+        file_name=file_name,
+        message_type=QueueMessageTypes.EFT_FILE_UPLOADED.value,
+    )
+    short_name_id = eft_short_name.id
+    eft_credit_balance = EFTCreditModel.get_eft_credit_balance(short_name_id)
+    assert eft_credit_balance == 150.50
+
+    short_name_links = EFTShortNamesService.get_shortname_links(short_name_id)
+    assert short_name_links["items"]
+    assert len(short_name_links["items"]) == 2
+
+    short_name_link = short_name_links["items"][0]
+    assert short_name_link.get("has_pending_payment") is False
+    assert short_name_link.get("amount_owing") == 150.50
+
+
 def test_skip_on_existing_pending_payments(session, app, client):
     """Test auto payment skipping payment when there exists a pending payment."""
     payment_account, eft_short_name, invoice = create_test_data()